Create a gist now

Instantly share code, notes, and snippets.

What would you like to do?
Script that converts TRK to TCK using
import os
import argparse
import nibabel as nib
def build_argparser():
DESCRIPTION = "Convert tractograms (TRK -> TCK)."
p = argparse.ArgumentParser(description=DESCRIPTION)
p.add_argument('tractograms', metavar='bundle', nargs="+", help='list of tractograms.')
p.add_argument('-f', '--force', action="store_true", help='overwrite existing output files.')
return p
def main():
parser = build_argparser()
args = parser.parse_args()
for tractogram in args.tractograms:
if nib.streamlines.detect_format(tractogram) is not nib.streamlines.TrkFile:
print("Skipping non TRK file: '{}'".format(tractogram))
output_filename = tractogram[:-4] + '.tck'
if os.path.isfile(output_filename) and not args.force:
print("Skipping existing file: '{}'. Use -f to overwrite.".format(output_filename))
trk = nib.streamlines.load(tractogram), output_filename)
if __name__ == '__main__':
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment